A Comparison of Deep Learning U Net Architectures For Posterior Segment OCT Retinal Layer Segmentation

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com/scientificreports
OPEN A comparison of deep learning

U‑Net architectures for posterior
segment OCT retinal layer
segmentation
Jason Kugelman1*, Joseph Allman1, Scott A. Read1, Stephen J. Vincent1, Janelle Tong2,3,
Michael Kalloniatis2,3, Fred K. Chen4,5,6, Michael J. Collins1 & David Alonso‑Caneiro1,4
Deep learning methods have enabled a fast, accurate and automated approach for retinal layer
segmentation in posterior segment OCT images. Due to the success of semantic segmentation
methods adopting the U-Net, a wide range of variants and improvements have been developed and
applied to OCT segmentation. Unfortunately, the relative performance of these methods is difficult to
ascertain for OCT retinal layer segmentation due to a lack of comprehensive comparative studies, and
a lack of proper matching between networks in previous comparisons, as well as the use of different
OCT datasets between studies. In this paper, a detailed and unbiased comparison is performed
between eight U-Net architecture variants across four different OCT datasets from a range of different
populations, ocular pathologies, acquisition parameters, instruments and segmentation tasks.
The U-Net architecture variants evaluated include some which have not been previously explored
for OCT segmentation. Using the Dice coefficient to evaluate segmentation performance, minimal
differences were noted between most of the tested architectures across the four datasets. Using an
extra convolutional layer per pooling block gave a small improvement in segmentation performance
for all architectures across all four datasets. This finding highlights the importance of careful
architecture comparison (e.g. ensuring networks are matched using an equivalent number of layers)
to obtain a true and unbiased performance assessment of fully semantic models. Overall, this study
demonstrates that the vanilla U-Net is sufficient for OCT retinal layer segmentation and that state-of-
the-art methods and other architectural changes are potentially unnecessary for this particular task,
especially given the associated increased complexity and slower speed for the marginal performance
gains observed. Given the U-Net model and its variants represent one of the most commonly applied
image segmentation methods, the consistent findings across several datasets here are likely to
translate to many other OCT datasets and studies. This will provide significant value by saving time
and cost in experimentation and model development as well as reduced inference time in practice by
selecting simpler models.
Optical coherence tomography (OCT) is a non-invasive, high resolution imaging modality that is commonly
used in ophthalmic imaging. By allowing easy visualisation of the retinal tissue, OCT scans can be employed by
clinicians and researchers for diagnosis of ocular diseases and monitoring disease progression or response to
therapy through the quantitative and qualitative analysis of features within these images. The inner and outer
boundaries of the retinal and choroidal layers are of particular interest in OCT image analysis. However, the
marking of the position of these boundaries can be slow and inefficient when performed manually by a human
expert annotator. Therefore, rapid and reliable automated algorithms are necessary to perform retinal segmenta-
tion in a time-efficient manner.
1
Contact Lens and Visual Optics Laboratory, Centre for Vision and Eye Research, School of Optometry and Vision
Science, Queensland University of Technology (QUT), Kelvin Grove, Australia. 2Centre for Eye Health, University
of New South Wales (UNSW), Sydney, NSW, Australia. 3School of Optometry and Vision Science, UNSW,
Sydney, NSW, Australia. 4Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The
University of Western Australia, Perth, WA, Australia. 5Department of Ophthalmology, Royal Perth Hospital,
Perth, WA, Australia. 6Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, Victoria,
Australia. *email: j.kugelman@qut.edu.au
Scientific Reports | (2022) 12:14888 | https://doi.org/10.1038/s41598-022-18646-2 1
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Variant Original Applications Key features

27 14,17,18,25
Vanilla U-Net Encoder-decoder, pixel-level semantic segmentation, skip connections
29,30 20,40,41
Dense U-Net Encourage feature reuse, avoid vanishing gradients, connect each output to all subsequent inputs within the block
31 42,43
Inception U-Net Multiple kernel sizes per layer, robust to images of different scales
32 26,44–46
Attention U-Net Focus more on important features, focus less on unimportant ones
33,34 14–16,47,14 Shortcut connections, easier to optimise residual compared to original, improve gradient flow, avoid performance degradation in
Residual U-Net
very deep networks
35 48
R2 U-Net Benefits of residual learning + feature accumulation and improved parameter utilisation
36
U-Net + + – Dense skip connections, improved feature aggregation
37–39 14,15,24
SE U-Net Spatial and channel recalibration, reweight spatial locations and feature maps (channels) based on importance
Table 1. Summary of the U-Net architectures compared in this study.
Early automatic methods for OCT retinal and choroidal segmentation relied upon standard image processing
techniques as part of methods that were handcrafted to suit particular sets of images1–9. While these methods
achieve the goal of saving time, the specific nature of the rules that make up their algorithms means that they
may not generalise well to other data without manually recalibrating the algorithm, which can take considerable
time and present notable difficulties. On the other hand, a range of alternative methods have been proposed
which are based on deep learning. A deep learning method can automatically learn the rules from a dataset,
rectifying one of the main drawbacks of traditional analysis techniques. Additionally, extending an algorithm
to new data typically requires simply extending the training set with the new samples, while most other training
and model parameters do not need to be modified for the method to operate. There are numerous deep learn-
ing methods that have been proposed for OCT retinal segmentation with a few different techniques commonly
employed including patch-based m ethods10–14 and semantic segmentation m ethods14–26, among others. Semantic
segmentation methods, in particular, have demonstrated state-of-the-art performance in retinal and choroidal
layer segmentation tasks of OCT i mages14.
The majority of semantic segmentation methods adopt an encoder-decoder deep neural network structure,
most of which base their architectures on the U-Net27, improving over the original fully-convolutional network
approach28. In the U-Net, skip connections improve gradient flow and allow the transfer of information between
the down-sampling and up-sampling paths by connecting each pair of encoder-decoder layers. The U-Net takes
an input OCT image and classifies each individual pixel in the image into one of several possible classes, thereby
segmenting the image into the different regions. For OCT retinal layer segmentation, the classes correspond
to the different tissue layers and other regions around the tissue layers of interest. The output of the U-Net is a
pixel-level map providing precise segmentation of the regions and layers of interest.
There are several variants which aim to improve performance compared to the original (vanilla) U-Net archi-
tecture. Dense U-Net29,30 connects all convolution block outputs to the inputs of all subsequent blocks within each
level which encourage feature reuse as well as aiding in preventing vanishing gradients. The Inception U-Net31
employs multiple convolutional kernel sizes in parallel paths at each level ensuring a greater level of robustness
to images of different scales. The Attention U-Net32 employs an attention module within each skip connection,
with these modules allowing for greater focus to be given to the more important spatial regions within an image
and lesser focus on those of lower importance. The residual U-Net33,34 adopts residual learning in each of the
layers by adding shortcut connections which aim to improve gradient flow and work under the theory that the
residual mapping is easier to learn than the original one. The recurrent-residual (R2) U-Net35 combines the ben-
efits of residual learning (see Residual U-Net) and recurrent connections, the latter of which allows for improved
feature accumulation and parameter utilisation. The U-Net++36 uses a set of dense skip connections allowing
for improved aggregation of features across different semantic scales. The squeeze + excite (SE) U-Net37–39 incor-
porates squeeze + excite blocks at the output of each convolutional block. These blocks allow for activation map
reweighting of both spatial locations and channels based on the relative importance of each spatial location and
channel. A summary of each architecture as well as references to their prior applications can be found in Table 1.
Previous studies for medical image segmentation (including OCT) have proposed a number of variants of
the U-net architecture to improve performance. However, the effect of these U-Net architectural changes on
OCT image segmentation performance is unclear, as an unbiased comparison across multiple OCT datasets has
not been performed. Indeed, previous comparisons use different datasets to one another, compare using only a
single dataset, compare only using a small subset of methods, and/or contain bias due to network architectures
not being properly matched (e.g. using a different number of layers to one another).
In this study, a comparison is performed using eight significant U-Net variants on four different and varied
OCT datasets to obtain an understanding of their effect on segmentation performance as well as trade-offs with
respect to computational time (training and evaluation) and complexity. The four OCT datasets encompass data
from a range of different populations, ocular pathologies, scanning parameters, instruments and segmentation
tasks, to ensure that the comparison is not biased and limited to just a single dataset. The effect of the number of
convolutional layers is also examined, by comparing two and three layers per block, as a simple complementary
experiment alongside the more complex architectural changes. The overall goal of this study is to determine
general conclusions for semantic OCT retinal layer segmentation using U-Net architectures which can be applied
to any OCT dataset and result in significant time savings for future studies. This study also examines network
architectures that have not previously been applied to this problem. To the best of our knowledge, the U-Net++,
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R2U-Net and Inception U-Net have not been previously applied to OCT retinal or choroidal segmentation and
hence will be investigated in this study.
Methods
Data. Four datasets were used in this study, which aim to provide a wide range of image qualities and fea-
tures. Thus, it will allow an improved understanding of the performance of the U-Net variants. For the relevant
ethics information, please refer to the original studies using the citations below. All methods were performed in
accordance with the relevant guidelines and regulations.
Dataset 1: Healthy. This dataset, from a previous study49, consists of spectral domain OCT (SD-OCT)
B-scans from 104 healthy children. Approval from the Queensland University of Technology human research
ethics committee was obtained before commencement of the study, and written informed consent was provided
by all participating children and their parents. All participants were treated in accordance with the tenets of the
Declaration of Helsinki. Data was sourced across four separate visits over a period of approximately 18 months,
however for the purposes of this study, we utilise data from the first visit only. For this visit, 6 cross-sectional
scans were acquired, equally spaced in a radial pattern, and centred upon the fovea. Scans were acquired using
the Heidelberg Spectralis SD-OCT instrument. For all scans, 30 frames were averaged using the inbuilt auto-
mated real time function (ART) to reduce noise while enhanced depth imaging (EDI) was used to improve
the visibility of the choroidal tissue. Each scan measures 1536 pixels wide by 496 pixels deep (approximately
8.8 × 1.9 mm respectively in physical dimensions with a vertical scale of 3.9 µm per pixel and a horizontal scale
of 5.7 µm per pixel). After data collection, all scans were annotated by an expert human observer with bound-
ary annotations created for three tissue layer boundaries including: the inner boundary of the inner limiting
membrane (ILM), the outer boundary of retinal pigment epithelium (RPE), and the choroid-sclera interface
(CSI). For each scan, a semantic segmentation mask (same pixel dimensions) is constructed with four regions:
(1) vitreous (all pixels between top of the image and the ILM), (2) retina (ILM to RPE), (3) choroid (RPE to CSI),
and (4) sclera (CSI to bottom of the image). An example scan and corresponding segmentation mask is provided
in Fig. 1. For the purposes of this study, the data was randomly divided into a training (40 participants, 240
scans total), validation (10 participants, 60 scans total) and testing set (49 participants, 294 scans total) with no
participant’s data overlapping between sets.
Dataset 2: Stargardt disease. This dataset, described in a prior study15, consists of SD-OCT scans of
patients with varying stages of Stargardt disease. Approval to identify and use SD-OCT images from patients with
genetically confirmed Stargardt disease for developing segmentation methods was obtained from the Human
Ethics Office of Research Enterprise, The University of Western Australia (RA/4/1/8932 and RA/4/1/7916) and
the Human Research Ethics Committee, Sir Charles Gairdner Hospital (2001-053). Scans were acquired from
18 participants, with 4 volumes (captured at different visits at different times) of ~ 50–60 B-scans from each. The
scans measure 1536 pixels wide by 496 pixels high, with a vertical scale of 3.9 µm per pixel and a horizontal scale
of 5.7 µm per pixel, this corresponds to an approximate physical area of size 8.8 × 1.9 mm (width × height). Scans
were acquired using the Heidelberg Spectralis SD-OCT instrument with the ART algorithm used to enhance the
definition of each B-scan by averaging nine OCT images. Scans were taken in high-resolution mode, unless it
was determined necessary to use high-speed mode owing to poor fixation (any low-resolution scan was resized
to match the resolution of the dataset). EDI was not employed. Contrast enhancement is utilised15,50 in an effort
to improve layer visibility and subsequently improve segmentation performance. After acquisition, each scan
was annotated by an expert human observer, with annotations provided for two layer boundaries including: the
inner boundary of the inner limiting membrane (ILM), and the outer boundary of the retinal pigment epithe-
lium (RPE). In some patients with Stargardt disease, the RPE and the outer retinal layers are lost in the central
region of the retina. In such cases, the remaining Bruch’s membrane (BM) that separates the residual inner retina
from the choroid is marked as the outer boundary. For each scan, a semantic segmentation mask is constructed
(same pixel dimensions) with three regions: (1) vitreous (all pixels from top of image to the ILM), (2) retina
(from ILM to RPE/BM) and (3) choroid/sclera (RPE/BM to bottom of the image). An example scan and cor-
responding segmentation mask is provided in Fig. 1. Each participant is categorised into one of two categories
based on retinal volume (low or high). This is calculated based on the total macular retinal volume based on
the boundary annotations such that there is an even number of participants in each category. For this study, the
data is divided into training (10 participants, 2426 scans), validation (2 participants, 486 scans), and testing (6
participants, 1370 scans) sets ensuring that there is an even split of low and high volume participants in each set.
Dataset 3: Age‑related macular degeneration. This dataset consists of OCT scans of patients exhib-
iting age-related macular degeneration (AMD)51. All scans were acquired using the Bioptigen SD-OCT with
data sourced from four different sites with scanning resolutions varying slightly between the sites52. No image
averaging is employed. A total of 269 participants are utilised, each with a single volume of 100 scans. However,
only a subset of the scans is used. A scan is used only if it contains at least 512 pixels (approximately half the
width) of available boundary annotations, otherwise it is discarded. Each scan is then cropped to a central 512
pixels horizontally with each scan also measuring 512 pixels in height (no cropping). Each scan is supplied with
boundary annotations for three layer boundaries including the inner boundary of the ILM, the outer boundary
of the retinal pigment epithelium drusen complex (RPEDC) and the outer boundary of BM. For each scan, a
semantic segmentation mask is constructed (same pixel dimensions) with four regions including: (1) vitreous
(all pixels from the top of the image to the ILM), (2) retina (ILM to RPEDC), (3) Bruch’s membrane (RPEDC to
BM), and (4) choroid/sclera (BM to bottom of the image). An example scan and corresponding segmentation
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Figure 1. Example OCT image and corresponding semantic segmentation mask for each of the four datasets.
Images are shown maintaining their aspect ratio. Each individual colour corresponds to a different region/class
as labelled. White dashed box in the topmost corresponds to the zoomed region (second and third images) for
each dataset.
mask is provided in Fig. 1. A total of 163 participants (4439 scans) are used for training, 54 participants (1481
scans) for validation, and 52 participants (1421 scans) for testing with all participants assigned randomly with
no overlap or duplication.
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Dataset 4: Widefield. This dataset, which has been described in detail elsewhere53, included 12 healthy
participants that had widefield OCT volume scans acquired using a widefield objective lens while maintaining
central fixation. All participants provided written consent as per protocols approved by the University of New
South Wales Australia Human Research Ethics Advisory panel, and the study adhered to the tenets of the Dec-
laration of Helsinki. Scans were acquired using the Heidelberg Spectralis where the applied scanning protocol
acquired 109 B-scans spaced 120 μm apart, spanning a total area of 55° horizontally and 45° vertically (15.84 mm
wide and 12.96 mm high), and ART was set to 16 to reduce noise. OCT B-scans were manually segmented to
extract two boundaries of interest: the inner boundary of the ganglion cell-inner layer (GCL), and the outer
boundary of the inner plexiform layer (IPL). The thickness data between these two boundaries (ganglion cell-
inner plexiform layer thickness) can inform the detection and screening of a number of retinal diseases such
as glaucoma54, central retinal vein occlusion55 and diabetic macular edema56. After resizing and cropping to the
region of interest, the scans measure 1392 pixels wide by 496 pixels high. For each scan, a semantic segmentation
mask is constructed (same pixel dimensions) with three regions: (1) all pixels from the top of the image to the
GCL, (2) all pixels between GCL and IPL, and (3) all pixels between the IPL and the bottom of the image. An
example scan and corresponding segmentation mask is provided in Fig. 1. Scans from a total of 12 participants
(~ 109 scans each, with one scan discarded from a single participant) are utilised with 6 participants assigned for
training (654 images total), 3 for validation (326 images total) and 3 for testing (327 images total). There is no
overlap of participants between the three sets.
Training and architecture parameters. All networks are trained to perform semantic segmentation of
the OCT scans. Using a 1 × 1 convolution layer (1 × 1 strides, filter count corresponding to number of regions)
followed by a softmax activation, the output of each network consists of class probabilities corresponding to
each pixel in the original input OCT image. For the Stargardt disease and widefield datasets, the probabilities
represent the classification of each pixel into one of three areas/regions of the OCT images, while there are
four such areas for the healthy and AMD datasets as described in the Data section. For each of the eight vari-
ants of the U-net architecture that are considered, we build off previous code implementations as follows: (1)
baseline57, (2) d
ense58, (3) attention59, (4) squeeze and excite (SE)60, (5) residual61, (6) recurrent-residual (R2)62,
(7) U-Net++63, and (8) Inception64. For the comparison in this study, all networks utilise max pooling layers
(2 × 2) for down-sampling and transposed convolutions for up-sampling (2 × 2 kernel and strides). Each network
consists of four pooling/up-sampling layers with 16 filters for all convolutions in the first layer which is doubled
after each pooling and subsequently halved at each up-sampling layer. Each convolution uses Glorot u niform65
kernel initialisation, and each layer, with the exception of the output layer, is followed by batch n ormalisation66
and a rectified linear unit activation. We compare two variants for each architecture by considering two and
three convolutions per layer. A visual summary of each architecture is given in Fig. 2. For the residual variant,
the ‘ReLU before addition’ block variant is selected while two recurrences are performed for the R2 variant. For
the SE variant, we employ the scSE module (concurrent cSE and sSE) with default ratio of 2 for the cSE compo-
nent. The U-Net++ architecture employs the same filters within the encoder and decoder (16 filters first layer,
subsequently doubled in each layer) as the other architectures. However, all the intermediate layers (between the
encoder and decoder) use 16 filters each, for computational reasons.
For training, the Adam o ptimizer67 is employed with default parameters (except for the learning rate which is
set at 0.0001). A batch size of two is used and all networks are trained for 200 epochs, minimising cross-entropy
as the training objective. For model selection, we use the epoch with the best Dice coefficient on the validation
set. The Dice coefficient is a measure of similarity between two samples (in this case, the predicted segmentation
map and ground truth map) and is defined as:
2TP
Dice = (1)
2TP + FP + FN
where TP: number of true positives, FP: number of false positives, and FN: number of false negatives.
For regularisation during training, all training samples are shuffled randomly at the beginning of each epoch.
No augmentation is employed for any experiments for simplicity. The comparison between architectures is
performed by comparing the Dice coefficient on the testing set using the model selected from the best epoch.
To perform a fair comparison between the network architectures, it is necessary to run each experiment several
times to ensure that there is no bias as a result of random weight initialisation and sample shuffling. Hence, all
experiments are performed three times in this study. All experiments are undertaken using Tensorflow 2.3.1 in
Python 3.7.4 using an NVIDIA M40 graphics processing unit (GPU).
To statistically compare the segmentation outcomes (Dice coefficient) from the different architectures, a
one-way repeated measures analysis of variance (ANOVA) was run for each of the different datasets for both the
2 layer and 3 layer variants separately, examining the within-subject effect of network architecture. Bonferroni-
adjusted pairwise comparisons were conducted to compare between specific network architectures. An additional
ANOVA was conducted to compare between the segmentation outcomes of the 2 layer and 3 layer variants.
Results
Tables 2, 3, 4 and 5 provide a summary of the main results for the healthy dataset, Stargardt disease dataset, AMD
dataset and widefield dataset, respectively. The accuracy represents the mean (and standard deviation) overall
Dice coefficient as the main performance metric, while the times (epoch training and evaluation time) together
with the number of parameters allow for a comparison of the computational complexity of the networks. Figure 3
provides a visual summary of accuracy vs. evaluation time vs. network complexity with a subplot for each of
the four datasets. It can be noted that the general clustering of the two-layer variants (squares) and three-layer
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Figure 2. Summary of the U-Net based architectures compared in this study. Each architecture is depicted with
two pooling layers for simplicity but each uses four pooling layers in our experiments. Arrows show direction
of information flow. Coloured blocks represent particular layers as per the legend. Note: The R2, Residual and
Dense variants are depicted with three convolutional layers per block (for improved visualisation) while the
others are all depicted with two (except for the Inception variant where the number of layers does not apply).
variants (circles) indicates that most architectures exhibit comparable segmentation accuracy (x-axis) with the
notable exception being the R2 variant (in yellow), which showed a marginal performance improvement. Addi-
tionally, the general difference between these two clusters (squares and circles) indicates that the three-layer
variant (circles) consistently outperforms the two-layer variant (squares), but only by a small amount. While
the R2 variant (yellow) is the most accurate, it is also the slowest with respect to evaluation time (y-axis) and
therefore lies in the top right corner of the subplots. However, this is not a general trend with the Inception
variant, for instance, lying in the top left corner of the subplots (slow but with relatively low accuracy compared
to the other variants). Observing the subplots, there does not appear to be any clear trends with respect to the
number of network parameters (relative sizes of the circles and squares). Figures 4, 5, 6, and 7 give some example
segmentation outputs overlaid with transparency on the original OCT scans and comparisons to ground truth
segmentation, demonstrating the robustness and accuracy of the segmentations for each of the four datasets
(healthy, Stargardt disease, AMD and widefield) respectively using the R2 U-Net (3 layer variant).
The repeated measures ANOVA revealed a significant effect of network architecture for both the healthy
and Stargardt disease datasets (for both the 2 and 3 layer variants). Although the magnitude of differences
were small, the R2 architecture was found to be statistically significantly more accurate compared to some of
the other architectures including the vanilla, attention, SE and residual U-Net architectures (all p < 0.05). There
were also statistically significant differences for each architecture comparing the two and three layer variants
with the three-layer variant being slightly but statistically significantly more accurate on both the healthy and
Stargardt disease datasets (p < 0.05). Additionally, it was found that using three layers (compared to two layers)
was significantly more accurate overall (not taking architecture into account) (p < 0.05) on the healthy, Stargardt
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Accuracy Mean epoch train time Parameters

Network architecture Conv/layer (SD) [%] (SD) [s] Median image evaluation time [msec] [×106]
2 99.10 (0.01) 41.46 (0.60) 128 1.95
Vanilla U-Net
3 99.20 (0.05) 54.33 (0.34) 138 2.93
2 99.08 (0.02) 46.36 (0.14) 133 2.71
Dense U-Net
3 99.20 (0.05) 72.88 (0.02) 155 5.44
2 99.12 (0.05) 53.00 (0.85) 137 1.99
Attention U-Net
3 99.23 (0.01) 66.65 (0.52) 148 2.98
2 99.08 (0.02) 57.92 (0.95) 143 2.06
SE U-Net
3 99.20 (0.06) 70.88 (0.27) 155 3.04
2 99.10 (0.04) 42.61 (0.07) 127 1.95
Residual U-Net
3 99.23 (0.02) 55.50 (0.12) 139 2.93
2 99.24 (0.02) 65.01 (1.04) 156 2.00
R2 U-Net
3 99.28 (0.01) 103.59 (0.23) 186 3.00
U-Net + + 99.12 (0.02) 93.23 (1.38) 165 2.05
Inception U-Net 99.10 (0.04) 108.31 (0.04) 182 4.62
Table 2. Comparison of results for the healthy dataset. (SD: standard deviation, s: seconds, SE:
squeeze + excite, R2: recurrent-residual). The best and poorest results for each are annotated in bold and
underline text respectively.

2 97.27 (0.07) 366.89 (1.09) 121 1.95
Vanilla U-Net
3 97.45 (0.03) 509.44 (1.11) 132 2.93
2 97.24 (0.02) 422.02 (0.61) 129 2.71
Dense U-Net
3 97.41 (0.07) 696.60 (5.07) 152 5.44
2 97.26 (0.01) 505.11 (3.91) 133 1.99
Attention U-Net
3 97.51 (0.03) 631.13 (2.50) 145 2.98
2 97.50 (0.07) 541.35 (5.45) 136 2.06
SE U-Net
3 97.55 (0.06) 674.84 (2.15) 148 3.04
2 97.24 (0.04) 388.44 (4.56) 124 1.95
Residual U-Net
3 97.41 (0.02) 524.82 (3.80) 136 2.93
2 97.57 (0.06) 605.62 (0.76) 151 2.00
R2 U-Net
3 97.67 (0.05) 1004.66 (3.46) 180 3.00
U-Net + + 97.26 (0.05) 885.71 (4.98) 160 2.05
Inception U-Net 97.19 (0.05) 1047.61 (3.95) 175 4.62
Table 3. Comparison of results for the Stargardt disease dataset. (SD: standard deviation, s: seconds, SE:
disease and widefield datasets. On the other hand, there were no statistically significant differences between
architectures for the AMD and widefield datasets (all p > 0.05). The lack of significance of the results on these
datasets is likely related to the more variable performance on the AMD dataset and the small number of par-
ticipants in the widefield dataset.
Discussion
In this study, eight different U-Net variants were compared for their segmentation performance on four different
OCT image datasets encompassing a range of ocular pathologies and scanning parameters. Each architecture was
also compared using both two and three convolutional blocks per layer. The results suggest that there is largely
comparable performance (measured using Dice coefficient) for all of the architectures on the individual datasets.
Indeed, despite the increased complexity and running time of a number of the U-Net variants, their performance
was not notably greater than the baseline vanilla U-Net, which already exhibits excellent performance for OCT
retinal layer segmentation.
The eight U-Net architectures were similar in terms of accuracy, and the performance of each improved
slightly on all four datasets by using an additional convolutional layer per block (three instead of two), a com-
paratively simple architectural change. However, this was again at the cost of increased complexity and running
time as a result of the extra parameters introduced by the additional layers. Despite the resultant performance
improvements for each individual network, the comparison between each of them remains relatively unchanged.
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2 98.86 (0.63) 252.74 (0.88) 89 1.95
Vanilla U-Net
3 99.42 (0.29) 339.31 (0.11) 92 2.93
2 99.51 (0.07) 291.18 (2.37) 90 2.71
Dense U-Net
3 99.59 (0.03) 463.66 (1.71) 100 5.44
2 99.43 (0.21) 341.10 (5.71) 94 1.99
Attention U-Net
3 99.60 (0.02) 427.15 (7.47) 96 2.98
2 99.57 (0.02) 388.54 (4.60) 97 2.06
SE U-Net
3 99.60 (0.02) 468.74 (4.84) 101 3.04
2 99.15 (0.54) 268.15 (4.26) 88 1.95
Residual U-Net
3 99.49 (0.13) 352.40 (3.42) 92 2.93
2 99.56 (0.01) 409.71 (1.43) 99 2.00
R2 U-Net
3 99.63 (0.02) 671.08 (3.52) 111 3.00
U-Net + + 99.46 (0.05) 588.80 (2.19) 104 2.05
Inception U-Net 99.10 (0.33) 686.44 (2.89) 110 4.62
Table 4. Comparison of results for the AMD dataset. SD: standard deviation, s: seconds, SE: squeeze +
excite, R2: recurrent-residual). The best and poorest results for each are annotated in bold and underline text
respectively.

Network architecture Conv/layer (SD) [%] (SD) [sec] Median image evaluation time [msec] [×106]
2 99.19 (0.03) 102.34 (1.58) 113 1.95
Vanilla U-Net
3 99.46 (0.02) 138.03 (1.98) 124 2.93
2 99.21 (0.04) 122.12 (0.27) 124 2.71
Dense U-Net
3 99.43 (0.03) 192.76 (0.97) 141 5.44
2 99.17 (0.06) 136.72 (0.04) 125 1.99
Attention U-Net
3 99.42 (0.06) 171.68 (3.00) 134 2.98
2 99.25 (0.02) 146.67 (0.46) 128 2.06
SE U-Net
3 99.40 (0.06) 181.86 (1.79) 139 3.04
2 99.16 (0.04) 108.19 (1.31) 116 1.95
Residual U-Net
3 99.44 (0.02) 140.31 (0.43) 126 2.93
2 99.42 (0.04) 165.19 (1.38) 141 2.00
R2 U-Net
3 99.52 (0.07) 267.28 (0.63) 175 3.00
U-Net + + 99.21 (0.01) 234.88 (1.14) 149 2.05
Inception U-Net 99.10 (0.13) 277.68 (1.35) 163 4.62
Table 5. Comparison of results for the widefield dataset. (SD: standard deviation, s: seconds, SE:
That is, their relative performance to one another is comparable as it is with two convolutional layers. The find-
ings further highlight the importance of comparisons between different network architectures being performed
carefully (e.g. using the same number of layers). For instance, a vanilla U-Net and a Residual U-Net are often
fitted (by default) with two and three convolutional layers per block, respectively, which will potentially bias the
performance of the Residual U-Net. In this specific scenario, the additional layer is the cause of improvement
as opposed to the addition of residual connections. It may be possible for additional layers (e.g. 4 or more) to
be added to further improve performance, however, this is at the cost of drastically increased model complexity
as well as slower inference and training time. At a certain point, this increased complexity will also result in the
inability of the computing hardware to handle the model size (i.e. insufficient VRAM). Additionally, we hypoth-
esise that diminishing returns are likely with respect to performance (given the excellent performance with 3
layers) making the trade-off between performance and complexity even less favourable with higher numbers of
convolutional layers.
While segmentation accuracy (Dice coefficient) is a critical metric, it is not the only one that should be con-
sidered when comparing these architectures. Indeed, training time, evaluation speed, and model complexity are
some other vital factors to consider from the perspective of real-world training and model deployment both in
research and clinical practice. Small performance improvements may not be worthwhile in certain applications if
this is obtained at the cost of significantly increased complexity and reduced speed. In this case, while the vanilla
U-Net is the fastest to train, one of the fastest to evaluate, and possesses the fewest parameters (lowest complex-
ity), its performance is still comparable and competitive with the majority of the other architectures across all
Vol:.(1234567890)
Figure 3. Segmentation accuracy (horizontal axis) vs. evaluation speed (vertical axis) vs. network parameters
(size of symbol) for each of the datasets for two and three layers (square and circle symbols respectively) for each
architecture tested. Note: the axis scales on each subplot differ to support optimal visualisation.
datasets. On the other hand, the R2 U-Net performs slightly better and contains only slightly more parameters
but is significantly slower to train and evaluate as a result of the recurrences where layers are reused, requiring
additional computation at each step. In fact, it is the slowest to evaluate of any of the architectures highlighting a
key trade-off when selecting this architecture. Overall, the Inception U-Net does not perform favourably in any
metric possessing significantly more parameters than most of the other networks, being the slowest to train and
one of the slowest to evaluate, and yielding comparable performance on all of the datasets. Similarly, although
the Dense U-Net uses more parameters than most of the other networks (as it takes in more feature maps in the
subsequent dense block layers), its performance is only comparable across all four datasets. As expected, there
is a high correlation between training and evaluation time but there are a few minor exceptions. Although the
Inception U-Net is the slowest to train, the R2 U-Net (3 layer variant) is the slowest to evaluate across all four
datasets. This is likely due to differences in the type of operations that are performed in the forward pass (used
in evaluation) vs. in backpropagation (not used in evaluation). Based on these findings there is clear a trade-off
between memory, training time, evaluation speed, and performance. However, the improvements in performance
are small across all tested datasets and models, suggesting that simpler, faster models are the optimal choices for
OCT retinal layer segmentation.
The general level of performance between the datasets varies. However, this is expected given the higher
difficulty and subjectivity associated with images exhibiting pathology and with poorer image quality (i.e. vary-
ing noise levels). The comparison between architectures on some datasets told a slightly different story in some
cases. For instance, we observe a small benefit to using the squeeze + excitation U-Net on the Stargardt disease
dataset, similar to a previous study15. It appears that the recalibration of feature maps is beneficial in the presence
of highly pathological data and where the overall segmentation accuracies (Dice coefficients) are notably lower
than the other datasets. However, the overall level of improvement is small. In general, the performance between
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Figure 4. Example segmentation outputs from the R2 U-Net (3 layer variant) for the healthy dataset overlaid on
the images. Left: full image with grey dashed rectangle corresponding to the zoomed area of the two rightmost
images. Blue region: retina, red region: choroid, yellow region: sclera. Dotted lines correspond to the boundary
position ground truths.
Figure 5. Example segmentation outputs from the R2 U-Net (3 layer variant) for the Stargardt disease dataset
overlaid on the images. Left: full image with grey dashed rectangle corresponding to the zoomed area of the two
rightmost images. Blue region: retina, purple region: choroid + sclera. Dotted lines correspond to the boundary
position ground truths.
the three runs for each experiment was largely consistent, with standard deviations of less than 0.1% on three
of the four datasets with respect to the Dice coefficient. However, the performance on the AMD dataset shows
greater variability, particularly for the case of two convolutional layers on some of the architectures. Indeed,
the vanilla, residual, attention and inception variants all exhibited standard deviations > 0.2% when outfitted
with two convolutional layers. Adding a third convolutional layer showed a marked reduction in variability on
all architectures (except Inception, where the number of layers does not apply). We hypothesise that this vari-
ability is caused by the greater noise present in the AMD dataset, with this problem rectified significantly with
the increased network learning capacity (i.e. by adding an extra layer). We note that there are also differences in
the training and inference speeds for each of the different datasets which are associated with differing quanti-
ties of data and different sized images respectively. However, these differences are irrelevant for an architectural
comparison which examines a single dataset at a time, and has no effect on the overall conclusions of this study.
Vol:.(1234567890)
Figure 6. Example segmentation outputs from the R2 U-Net (3 layer variant) for the AMD dataset overlaid on
the images. Left: full image with grey dashed rectangle corresponding to the zoomed area of the two rightmost
images. Red region: retina (excluding BM), light purple region: BM, dark purple region: choroid + sclera. Dotted
lines correspond to the boundary position ground truths.
Figure 7. Example segmentation outputs from the R2 U-Net (3 layer variant) for the widefield dataset
overlaid on the images. Left: full image with grey dashed rectangle corresponding to the zoomed area of the
two rightmost images. Bright green region: GCL-IPL, dark green region: retina (below IPL) + choroid + sclera.
Dotted lines correspond to the boundary position ground truths.
In this study, four datasets were employed that are highly representative of real world OCT datasets that may
be encountered in practice. These are also similar to those used in other studies involving deep learning based
OCT segmentation m ethods11,12,14,15. Some of these datasets contain only a few participants, indicative of the
common difficulty of sourcing large numbers of participants due to privacy and confidentiality reasons as well
as a lack of readily available patients exhibiting less common ocular pathologies. However, a significant number
of scans from each of these patients are used, to support invariance of the model to patient agnostic image fea-
tures and artefacts, such as speckle noise. Despite potential issues surrounding a low number of participants and
model bias, the performance of all models is excellent across all datasets suggesting that this does not degrade
the performance. Additionally, the findings from the architectural comparison on each dataset are largely com-
parable, demonstrating that the lower quantity of data on some datasets does not appear to be biasing the results
Vol.:(0123456789)
or invalidating the findings of this study. This also further supports the previously demonstrated fact that the
U-Net can be trained well even with a relatively small number of images27.
Here, there was an exclusive focus on an architectural comparison between U-Net variants for OCT semantic
segmentation of retinal layers. We stress that there are other OCT segmentation methods that have not been
considered here. These specific methods are not considered as they incorporate other changes and modifications
beyond the architecture (e.g. loss function, class weighting, additional post-processing etc.) which are outside
the scope of this study. For instance, another s tudy68 has performed a comparison between traditional (Dice
and logistic) and adversarial (GAN) losses. Future studies should examine other such parameters and perform
similar comparisons. There are also numerous other configurations of U-Net architectures (e.g. different residual
block configurations, number of recurrences) and other semantic segmentation architectures (e.g. DeepLabv3+69,
SegNet70) that have not been tested here to retain a manageable scope for this study. An interesting direction for
future work could be to examine an ensemble approach using different U-Net architectures for each ensemble
member. However, given the largely comparable performance between the tested architectures in this study, we
speculate that any performance benefits may be minor.
Conclusion
In this study, we have performed a comprehensive, unbiased comparison of U-Net architecture variants for the
application of semantic segmentation in retinal OCT images across several datasets. All tested U-Net architec-
tures provide excellent performance for OCT retinal layer segmentation, and the results suggest that there is
little notable difference in performance between them when evaluated using the Dice metric. There are expected
trade-offs between performance, speed and complexity that are important to consider depending on the particu-
lar clinical and research application as well as constraints on time and available hardware. The findings of this
study also highlight the importance of careful and unbiased comparisons of deep learning methods and correctly
matching network architectures to obtain a true understanding on the impact of network architectural changes.
Overall, the significantly increased complexity and reduced speed of the U-Net variants with only marginal per-
formance gains suggest that the baseline vanilla U-Net is an optimal choice for OCT retinal layer segmentation
in practice. State-of-the-art models do not appear to provide a clear benefit for this application while increasing
the number of layers in each model resulted in small performance gains but, again, with a trade-off with respect
to complexity and speed. A significant time investment in any study involving deep learning is that of model
comparison and optimal selection. The findings in this study can help to provide a solid, well-informed start-
ing point, alleviating the time and cost burden of experimental comparison in future studies while also guiding
model selection towards simpler and faster models. The findings here are largely consistent across several varied
OCT datasets with differing pathologies, instruments, scanning parameters and segmentation tasks. Therefore,
these can be generalised and are likely transferable to a wide range of other OCT datasets further highlighting
the benefit of this study for future work with U-Net based models for OCT retinal layer segmentation which are
commonly employed for this application.
Data availability
The healthy, Stargardt disease and widefield datasets analysed during the current study are currently not publicly
available. However, the algorithms and code used throughout this study are publicly and readily available at
https://github.com/jakugel/unet-variants.
Received: 31 March 2022; Accepted: 17 August 2022
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Acknowledgements
Computational resources and services used in this work were provided in part by the HPC and Research Support
Group, Queensland University of Technology, Brisbane, Australia. We gratefully acknowledge support from the
NVIDIA Corporation for the donation of GPUs used in this work. This work was supported by Ideas Grants and
a Fellowship from the Australian National Health and Medical Research Council of Australia [GNT1186915,
GNT1116360 (FC) and MRF1142962 (FC)], a scholarship from the Australian Government Research Training
Program (JT), and project grants from the Telethon-Perth Children’s Hospital Research Fund (DAC, FC), and the
Macular Disease Foundation Australia (FC). Additionally, Guide Dogs NSW/ACT provided a PhD scholarship
(JT), salary support (JP and MK) and support clinical service delivery at the Centre for Eye Health. The funding
bodies had no role in the conceptualization or writing of the paper.
Author contributions
Design of the research: D.A.C., J.K. Software development: J.A., J.K. Analysis and interpretation of data: J.K.,
D.A.C., S.A.R., J.A. Drafting the manuscript: J.K., D.A.C. Reviewed and approved final manuscript: J.K., J.A.,
S.A.R., S.J.V, J.T., M.K., F.K.C., M.J.C., D.A.C.
Competing interests
The authors declare no competing interests.
Additional information
Correspondence and requests for materials should be addressed to J.K.
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OPEN A comparison of deep learning

Scientific Reports | (2022) 12:14888 | https://doi.org/10.1038/s41598-022-18646-2 1

Variant Original Applications Key features

Table 1. Summary of the U-Net architectures compared in this study.

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Accuracy Mean epoch train time Parameters

Accuracy Mean epoch train time Parameters

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Accuracy Mean epoch train time Parameters

Accuracy Mean epoch train time Parameters

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Received: 31 March 2022; Accepted: 17 August 2022

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© The Author(s) 2022

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Table 1. Summary of the U-Net architectures compared in this study.